I posted this already but since it offers some kind of conclusion abbout the topic, I figured I would repost it here so than it can be better seen:

This would be a very good solution indeed if my module was object oriented...
I found some stuff about why what I wanted to do isn't possible on : Name Collision of Modules and libs
A very interesting reading for us mod_perl users.
Now I think i will use a method based on the previous link: Config Files, using a hash with a key for each vHost.
This seems the most sensible appproach.

It's (only?) drawback I guess it that there will have some many hash lookups which could hit performance, but on the other hand it will save a lot of memory since I won't have to export as many symbols.